Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3 - PubMed (original) (raw)
doi: 10.1038/ng1563. Epub 2005 May 15.
Alika K Maunakea, Peter Jun, Chibo Hong, Giuseppe Zardo, Daniel Pinkel, Donna G Albertson, Jane Fridlyand, Jian-Hua Mao, Ksenya Shchors, William A Weiss, Joseph F Costello
Affiliations
- PMID: 15895082
- DOI: 10.1038/ng1563
Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3
Tsui-Ting Ching et al. Nat Genet. 2005 Jun.
Abstract
CpG islands are present in one-half of all human and mouse genes and typically overlap with promoters or exons. We developed a method for high-resolution analysis of the methylation status of CpG islands genome-wide, using arrays of BAC clones and the methylation-sensitive restriction enzyme NotI. Here we demonstrate the accuracy and specificity of the method. By computationally mapping all NotI sites, methylation events can be defined with single-nucleotide precision throughout the genome. We also demonstrate the unique expandability of the array method using a different methylation-sensitive restriction enzyme, BssHII. We identified and validated new CpG island loci that are methylated in a tissue-specific manner in normal human tissues. The methylation status of the CpG islands is associated with gene expression for several genes, including SHANK3, which encodes a structural protein in neuronal postsynaptic densities. Defects in SHANK3 seem to underlie human 22q13 deletion syndrome. Furthermore, these patterns for SHANK3 are conserved in mice and rats.
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